Submissions for variant NM_015599.3(PGM3):c.378dup (p.Arg127Ter)

Minimum review status:		Collection method:
Minimum conflict level: Report conflict between different conditions
		ClinVar version:

Total submissions: 4

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Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Labcorp Genetics (formerly Invitae), Labcorp	RCV001914469	SCV002141660	pathogenic	Immunodeficiency 23	2024-02-14	criteria provided, single submitter	clinical testing	This sequence change creates a premature translational stop signal (p.Arg155*) in the PGM3 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PGM3 are known to be pathogenic (PMID: 17548465, 24589341, 24931394). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with PGM3-related conditions. ClinVar contains an entry for this variant (Variation ID: 1377883). For these reasons, this variant has been classified as Pathogenic.
Neuberg Centre For Genomic Medicine, NCGM	RCV001914469	SCV004175839	likely pathogenic	Immunodeficiency 23	2023-02-14	criteria provided, single submitter	clinical testing	The frameshift c.378dup(p.Arg127Ter) variant in PGM3 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. This variant is novel (not in any individuals) in gnomAD Exomes and 1000 Genomes. This variant has been reported to the ClinVar database as Pathogenic. However, study in multiple affected individuals and functional evidence on its pathogenicity is not available. This variant is predicted to cause loss of normal protein function through protein truncation. Loss of function variants have been previously reported to be disease causing. For these reasons, this variant has been classified as Likely Pathogenic. In the absence of another reportable variant, the molecular diagnosis is not confirmed.
Revvity Omics, Revvity	RCV001914469	SCV004238337	likely pathogenic	Immunodeficiency 23	2023-07-18	criteria provided, single submitter	clinical testing
Fulgent Genetics, Fulgent Genetics	RCV001914469	SCV005674026	likely pathogenic	Immunodeficiency 23	2024-05-25	criteria provided, single submitter	clinical testing

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